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We validate our method in clonal cells with formerly defined integration sites and further demonstrate the ability to measure lentiviral integration websites and chromatin availability of number and viral genomes at the single-cell resolution in CAR-T cells. We anticipate that EpiVIA will enable the single-cell deconstruction of gene regulation during CAR-T therapy, ultimately causing the finding of cellular facets associated with durable therapy. Copyright © 2020 the Author(s). Published by PNAS